The current implementation for the
@sensitivity slot in a
PharmacoSet has some
Firstly, it does not natively support dose-response experiments with multiple drugs and/or cancer cell lines. As a result we have not been able to include this data into a PharmacoSet thus far.
Secondly, drug combination data has the potential to scale to high dimensionality. As a result we need an object that is highly performant to ensure computations on such data can be completed in a timely manner.
The current use case is supporting drug and cell-line combinations in
PharmacoGx, but we wanted to create something flexible enough to fit
other use cases. As such, the current class makes no mention of drugs or cell-lines,
nor anything specifically related to Bioinformatics or Computation Biology. Rather, we tried to design a general purpose data structure which could support
high dimensional data for any use case.
Our design takes the best aspects
MultiAssayExperiment class and implements
them using the
data.table package, which provides an R API to a rich set of
tools for high performance data processing implemented in C.
We have borrowed directly from the
assays slot names.
We also implemented the
SummarizedExperiment accessor generics for the
There are, however, some important differences which make this object more flexible when dealing with high dimensional data.